Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007922.1 Hibiscus syriacus cultivar Beakdansim tig00110327_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 874983
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:167121 original size:108 final size:110
Alignment explanation
Indices: 166911--167190 Score: 474
Period size: 108 Copynumber: 2.6 Consensus size: 110
166901 CTCGAACAAT
*
166911 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
166976 AATCGCGTCTGCCCCTTATTTATTCAGAGAGTATAAGACTCGAAC
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* *
167021 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CACAATCTTCATC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
167084 AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAT
66 AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
* *
167129 AATCTTCAACGATCGCGTCTGCCCCCAATTTATTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
167191 TTTTGCTTCA
Statistics
Matches: 159, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
108 99 0.62
109 4 0.03
110 56 0.35
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (110 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
AATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:168350 original size:1 final size:1
Alignment explanation
Indices: 168341--168411 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
168331 TGAACCCCCC
* * * * * * ** *
168341 TTTTATTTTTTATTTTTTTTTTCTTCTTTTTTTTTTTATTTTTTTTATTTTTTTCATTTTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
168406 TTTTTT
1 TTTTTT
168412 ATCTTTAAGC
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:168353 original size:7 final size:7
Alignment explanation
Indices: 168341--168409 Score: 70
Period size: 7 Copynumber: 9.6 Consensus size: 7
168331 TGAACCCCCC
168341 TTTTATT
1 TTTTATT
168348 TTTTATT
1 TTTTATT
168355 TTTT-TT
1 TTTTATT
*
168361 TTCTTCTT
1 TT-TTATT
168369 TTTT-TT
1 TTTTATT
*
168375 TTTATTTT
1 TTT-TATT
168383 TTTTATTT
1 TTTTA-TT
168391 TTTTCATT
1 TTTT-ATT
168399 TTTTATT
1 TTTTATT
168406 TTTT
1 TTTT
168410 TTATCTTTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
6 9 0.16
7 24 0.44
8 21 0.38
9 1 0.02
ACGTcount: A:0.09, C:0.04, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:168360 original size:9 final size:9
Alignment explanation
Indices: 168346--168413 Score: 81
Period size: 9 Copynumber: 7.9 Consensus size: 9
168336 CCCCCTTTTA
168346 TTTTTTATT
1 TTTTTTATT
168355 TTTTTT-TT
1 TTTTTTATT
*
168363 CTTCTTT-TT
1 -TTTTTTATT
168372 TTTTTTATT
1 TTTTTTATT
168381 TTTTTTATT
1 TTTTTTATT
*
168390 TTTTTCA--
1 TTTTTTATT
168397 TTTTTTATT
1 TTTTTTATT
168406 TTTTTTAT
1 TTTTTTAT
168414 CTTTAAGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
7 6 0.12
8 7 0.14
9 38 0.75
ACGTcount: A:0.09, C:0.04, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTATT
Found at i:168382 original size:25 final size:26
Alignment explanation
Indices: 168340--168416 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
168330 TTGAACCCCC
*
168340 CTTTTATTTTTTATTTTTTTTTTCTT
1 CTTTTATTTTTTATTTTTTTTATCTT
*
168366 CTTTTTTTTTTTATTTTTTTTAT-TT
1 CTTTTATTTTTTATTTTTTTTATCTT
168391 -TTTTCATTTTTTATTTTTTTTATCTT
1 CTTTT-ATTTTTTATTTTTTTTATCTT
168417 TAAGCAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
24 4 0.09
25 19 0.41
26 23 0.50
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.84
Consensus pattern (26 bp):
CTTTTATTTTTTATTTTTTTTATCTT
Found at i:169558 original size:3 final size:3
Alignment explanation
Indices: 169544--169575 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
169534 GTACCAAGGC
169544 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT C
169576 AATACTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:176931 original size:14 final size:15
Alignment explanation
Indices: 176910--176959 Score: 68
Period size: 14 Copynumber: 3.5 Consensus size: 15
176900 TTAATAATAC
176910 TAATAATTGTTATAA
1 TAATAATTGTTATAA
176925 T-ATAATTGTTATAA
1 TAATAATTGTTATAA
**
176939 TAATAA-TAATATAA
1 TAATAATTGTTATAA
176953 TAATAAT
1 TAATAAT
176960 ATAATAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 26 0.84
15 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (15 bp):
TAATAATTGTTATAA
Found at i:176943 original size:3 final size:3
Alignment explanation
Indices: 176935--176985 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
176925 TATAATTGTT
* *
176935 ATA ATA ATA ATA AT- ATA ATA ATA AT- ATA ATA GTA ATA ATT ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
176980 ATA ATA
1 ATA ATA
176986 TTTATAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:176954 original size:11 final size:11
Alignment explanation
Indices: 176938--176985 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
176928 AATTGTTATA
176938 ATAATAATAAT
1 ATAATAATAAT
176949 ATAATAATAAT
1 ATAATAATAAT
*
176960 ATAATAGT-A-
1 ATAATAATAAT
*
176969 ATAATTATAAT
1 ATAATAATAAT
176980 ATAATA
1 ATAATA
176986 TTTATAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 23 0.74
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:176960 original size:14 final size:14
Alignment explanation
Indices: 176934--176985 Score: 68
Period size: 14 Copynumber: 3.5 Consensus size: 14
176924 ATATAATTGT
176934 TATAATAATAATAA
1 TATAATAATAATAA
176948 TATAATAATAATATAA
1 TATAATAAT-A-ATAA
*
176964 TAGTAATAATTATAA
1 TA-TAATAATAATAA
176979 TATAATA
1 TATAATA
176986 TTTATAACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 14 0.41
15 7 0.21
16 6 0.18
17 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TATAATAATAATAA
Found at i:176985 original size:20 final size:19
Alignment explanation
Indices: 176903--176986 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
176893 CCTGATATTA
*
176903 ATAATACTAATAATTGT--T
1 ATAATA-TAATAATTATAAT
**
176921 ATAATATAATTGTTATAAT
1 ATAATATAATAATTATAAT
*
176940 AATAATA-ATATAATAATAAT
1 -ATAATATA-ATAATTATAAT
176960 ATAATAGTAATAATTATAAT
1 ATAATA-TAATAATTATAAT
176980 ATAATAT
1 ATAATAT
176987 TTATAACCAG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.13
18 6 0.11
19 9 0.17
20 30 0.57
21 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.42
Consensus pattern (19 bp):
ATAATATAATAATTATAAT
Found at i:176990 original size:14 final size:13
Alignment explanation
Indices: 176919--176992 Score: 62
Period size: 14 Copynumber: 5.5 Consensus size: 13
176909 CTAATAATTG
*
176919 TTATAATATAATTG
1 TTATAATATAA-TA
176933 TTATAATAATAATA
1 TTATAAT-ATAATA
*
176947 ATAT-A-ATAATA
1 TTATAATATAATA
*
176958 ATATAATAGTAATAA
1 TTATAATA-TAAT-A
176973 TTATAATATAATA
1 TTATAATATAATA
176986 TTTATAA
1 -TTATAA
176993 CCAGGACAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
11 10 0.20
12 1 0.02
13 3 0.06
14 25 0.49
15 12 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
TTATAATATAATA
Found at i:180041 original size:12 final size:13
Alignment explanation
Indices: 180018--180042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180008 TAACCCCCTA
180018 CCAAACCTTTTTG
1 CCAAACCTTTTTG
180031 CCAAACCTTTTT
1 CCAAACCTTTTT
180043 ATTCCAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (13 bp):
CCAAACCTTTTTG
Found at i:185373 original size:16 final size:16
Alignment explanation
Indices: 185352--185384 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
185342 TAATAAATAA
185352 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
185368 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
185384 A
1 A
185385 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:185465 original size:10 final size:10
Alignment explanation
Indices: 185450--185489 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
185440 CATTTAAATG
185450 ATAAACGAAC
1 ATAAACGAAC
185460 ATAAACGAAC
1 ATAAACGAAC
*
185470 GTAAACGAAC
1 ATAAACGAAC
*
185480 ACAAACGAAC
1 ATAAACGAAC
185490 GAACATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:185476 original size:20 final size:20
Alignment explanation
Indices: 185451--185490 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
185441 ATTTAAATGA
*
185451 TAAACGAACATAAACGAACG
1 TAAACGAACACAAACGAACG
185471 TAAACGAACACAAACGAACG
1 TAAACGAACACAAACGAACG
185491 AACATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.15, T:0.07
Consensus pattern (20 bp):
TAAACGAACACAAACGAACG
Found at i:185813 original size:14 final size:14
Alignment explanation
Indices: 185794--185860 Score: 88
Period size: 14 Copynumber: 5.1 Consensus size: 14
185784 GTCCTCTGTT
185794 CGAACATAAATGAA
1 CGAACATAAATGAA
185808 CGAACATAAAT---
1 CGAACATAAATGAA
185819 -GAACATAAATGAA
1 CGAACATAAATGAA
185832 CGAACATAAATGAA
1 CGAACATAAATGAA
* *
185846 CGCACATAAACGAA
1 CGAACATAAATGAA
185860 C
1 C
185861 ATATAATCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
10 10 0.21
14 37 0.79
ACGTcount: A:0.55, C:0.18, G:0.13, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:185824 original size:24 final size:24
Alignment explanation
Indices: 185795--185846 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
185785 TCCTCTGTTC
185795 GAACATAAATGAACGAACATAAAT
1 GAACATAAATGAACGAACATAAAT
185819 GAACATAAATGAACGAACATAAAT
1 GAACATAAATGAACGAACATAAAT
185843 GAAC
1 GAAC
185847 GCACATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.15
Consensus pattern (24 bp):
GAACATAAATGAACGAACATAAAT
Found at i:185857 original size:24 final size:24
Alignment explanation
Indices: 185801--185873 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
185791 GTTCGAACAT
* **
185801 AAATGAACGAACATAAATGAACAT
1 AAATAAACGAACATAAATGAACGC
*
185825 AAATGAACGAACATAAATGAACGC
1 AAATAAACGAACATAAATGAACGC
*
185849 ACATAAACGAACATATAATCGAACG
1 AAATAAACGAACATA-AAT-GAACG
185874 TTCACGAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 35 0.81
25 3 0.07
26 5 0.12
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.15
Consensus pattern (24 bp):
AAATAAACGAACATAAATGAACGC
Found at i:197350 original size:2 final size:2
Alignment explanation
Indices: 197343--197370 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
197333 TGGAAATGAA
197343 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
197371 GAAATTCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:198048 original size:44 final size:44
Alignment explanation
Indices: 197985--198085 Score: 193
Period size: 44 Copynumber: 2.3 Consensus size: 44
197975 AGAAACTATC
197985 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
1 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
198029 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
1 CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
*
198073 CATCTATAATAGT
1 CACCTATAATAGT
198086 TACATATAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (44 bp):
CACCTATAATAGTACAAAATACAATAAAATTTGTAATTATAATT
Found at i:199836 original size:27 final size:27
Alignment explanation
Indices: 199806--199858 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
199796 AAAATAAGAG
*
199806 ATTTTAAGAATTTT-AATTTTTTTTTAA
1 ATTTTAA-AATTTTAAATATTTTTTTAA
199833 ATTTTAAAATTTTAAATATTTTTTTA
1 ATTTTAAAATTTTAAATATTTTTTTA
199859 TAAGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTAAAATTTTAAATATTTTTTTAA
Found at i:204163 original size:21 final size:21
Alignment explanation
Indices: 204139--204178 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
204129 CCTGCATGGG
204139 GCAACAATAAAGCTGCAATTT
1 GCAACAATAAAGCTGCAATTT
* * *
204160 GCAATAATAATGTTGCAAT
1 GCAACAATAAAGCTGCAAT
204179 AATAACAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
GCAACAATAAAGCTGCAATTT
Found at i:204288 original size:3 final size:3
Alignment explanation
Indices: 204271--204372 Score: 102
Period size: 3 Copynumber: 32.7 Consensus size: 3
204261 GAGATAAAAT
204271 AAG AA- AAG AAG -AG AAG AAG AAGG AAG AAG AAG AAAG AAG AAAG AAAG
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG -AAG AAG -AAG -AAG
* *
204318 AAG AAG AA- AAG AAG AAGG AAG AAAG TAAG AAG AAG GAG AAG AAA AAG
1 AAG AAG AAG AAG AAG AA-G AAG -AAG -AAG AAG AAG AAG AAG AAG AAG
204365 AAG AAG AA
1 AAG AAG AA
204373 ATAAGGAAGA
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
2 6 0.07
3 58 0.67
4 22 0.26
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:204299 original size:18 final size:18
Alignment explanation
Indices: 204276--204389 Score: 92
Period size: 18 Copynumber: 6.1 Consensus size: 18
204266 AAAATAAGAA
204276 AAGAAGAGAAGAAGAAGG
1 AAGAAGAGAAGAAGAAGG
204294 AAGAAGAAGAAAGAAGAAAGAAAG
1 AAGAAG-AG-AAGAAG-AAG---G
*
204318 AAGAAGAAAAGAAGAAGG
1 AAGAAGAGAAGAAGAAGG
204336 AAGAA-AGTAAGAAGAAGG
1 AAGAAGAG-AAGAAGAAGG
* *
204354 -AGAAGAAAAAGAAGAAGA
1 AAGAAG-AGAAGAAGAAGG
*
204372 AATAAG-GAAG-AGAAGG
1 AAGAAGAGAAGAAGAAGG
204388 AA
1 AA
204390 ACAATCAAGT
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
16 7 0.09
17 8 0.10
18 31 0.39
19 7 0.09
20 6 0.08
21 6 0.08
22 6 0.08
23 1 0.01
24 7 0.09
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (18 bp):
AAGAAGAGAAGAAGAAGG
Found at i:204302 original size:21 final size:20
Alignment explanation
Indices: 204276--204370 Score: 117
Period size: 21 Copynumber: 4.8 Consensus size: 20
204266 AAAATAAGAA
204276 AAGAAGAGAAGAAGAAGGAAG
1 AAGAAGA-AAGAAGAAGGAAG
*
204297 AAGAAGAAAGAAGAAAGAAAG
1 AAGAAGAAAGAAG-AAGGAAG
204318 AAGAAGAAAAGAAGAAGGAAG
1 AAGAAG-AAAGAAGAAGGAAG
*
204339 -A-AAGTAAGAAGAAGG-AG
1 AAGAAGAAAGAAGAAGGAAG
204356 AAGAA-AAAGAAGAAG
1 AAGAAGAAAGAAGAAG
204371 AAATAAGGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
17 2 0.03
18 20 0.30
19 5 0.08
20 7 0.11
21 25 0.38
22 7 0.11
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (20 bp):
AAGAAGAAAGAAGAAGGAAG
Found at i:204390 original size:29 final size:30
Alignment explanation
Indices: 204283--204390 Score: 96
Period size: 32 Copynumber: 3.5 Consensus size: 30
204273 GAAAAGAAGA
*
204283 GAAGAAGAAGGAAGAAGAAGAAAGAAGA-AAG
1 GAAGAAGAAGGAAAAAGAAG-AAGAA-ATAAG
* *
204314 AAAGAAGAAGAAAAGAAGAAGGAAGAAAGTAA-
1 GAAGAAGAAGGAAA-AAGAA-GAAGAAA-TAAG
*
204346 GAAGAAGGAGAAGAAAAAGAAGAAGAAATAAG
1 GAAGAA-GA-AGGAAAAAGAAGAAGAAATAAG
204378 GAAG-AGAAGGAAA
1 GAAGAAGAAGGAAA
204391 CAATCAAGTA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
29 5 0.08
30 2 0.03
31 16 0.25
32 26 0.41
33 10 0.16
34 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (30 bp):
GAAGAAGAAGGAAAAAGAAGAAGAAATAAG
Found at i:204620 original size:17 final size:18
Alignment explanation
Indices: 204585--204631 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
204575 GAGCGATGAC
204585 TTATTATTAAATAAAATA
1 TTATTATTAAATAAAATA
204603 TTATT-TTAGAAT-AAATA
1 TTATTATTA-AATAAAATA
204620 TTATTATTAAAT
1 TTATTATTAAAT
204632 GGTAGAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATTATTAAATAAAATA
Found at i:209970 original size:24 final size:24
Alignment explanation
Indices: 209937--210009 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
209927 TGTAGTTCCC
*
209937 CAGAATTACATCCATAAGGACTTA
1 CAGAACTACATCCATAAGGACTTA
**
209961 CAGAACTACATCCATATTGACTTA
1 CAGAACTACATCCATAAGGACTTA
* *
209985 CATAACTACATCTATAAGGACTTA
1 CAGAACTACATCCATAAGGACTTA
210009 C
1 C
210010 TCTAGACTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (24 bp):
CAGAACTACATCCATAAGGACTTA
Found at i:212653 original size:3 final size:3
Alignment explanation
Indices: 212645--212703 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
212635 TATTTTATAT
212645 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
212692 TAA TAA TAA TAA
1 TAA TAA TAA TAA
212704 GTCACGTCAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:213043 original size:2 final size:2
Alignment explanation
Indices: 213036--213073 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
213026 GAAACTTCTA
213036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
213074 GTTTATGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:232996 original size:2 final size:2
Alignment explanation
Indices: 232984--233016 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
232974 ATAAGTGCAC
232984 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233017 CATCAACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:233305 original size:21 final size:22
Alignment explanation
Indices: 233262--233362 Score: 107
Period size: 23 Copynumber: 4.5 Consensus size: 22
233252 ATAAATTGCA
233262 CCGAAGTG-CCACATAGAATGTC
1 CCGAAG-GACCACATAGAATGTC
233284 CCGAAGGACCACATAG-ATGTC
1 CCGAAGGACCACATAGAATGTC
* *
233305 CCGAAGGACCGCGTAGAAATGTC
1 CCGAAGGACCACATAG-AATGTC
** * *
233328 CTAAAGGACTACGTAGAATTGTC
1 CCGAAGGACCACATAGAA-TGTC
233351 CCGAAGGACCAC
1 CCGAAGGACCAC
233363 GTAAAACCCT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
21 20 0.30
22 16 0.24
23 30 0.45
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATGTC
Found at i:233481 original size:15 final size:15
Alignment explanation
Indices: 233461--233499 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
233451 TTTCAATTAT
*
233461 TCACATAGTTCCGTA
1 TCACATAGTTCCATA
*
233476 TCACATAG-ACCATA
1 TCACATAGTTCCATA
233490 TCACATAGTT
1 TCACATAGTT
233500 TATATCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (15 bp):
TCACATAGTTCCATA
Found at i:235953 original size:4 final size:4
Alignment explanation
Indices: 235944--235968 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
235934 TATTATACTA
235944 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
235969 GCTTCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:245038 original size:21 final size:18
Alignment explanation
Indices: 244996--245038 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
244986 ATCAGTACAT
*
244996 CCATAATTTCACAAAATA
1 CCATAATTTCAAAAAATA
245014 CCATAATTTCATAAAGAATTA
1 CCATAATTTCA-AAA-AA-TA
245035 CCAT
1 CCAT
245039 CTTTCCGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.52
19 2 0.10
20 2 0.10
21 6 0.29
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (18 bp):
CCATAATTTCAAAAAATA
Found at i:261084 original size:20 final size:21
Alignment explanation
Indices: 261059--261112 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
261049 GACCAACAAA
261059 TTCGCAACGCGAA-CTCCAAT
1 TTCGCAACGCGAATCTCCAAT
* *
261079 TTCGCAAC-CCAATTTCCAAT
1 TTCGCAACGCGAATCTCCAAT
261099 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
261113 TTGTAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (21 bp):
TTCGCAACGCGAATCTCCAAT
Found at i:261178 original size:20 final size:20
Alignment explanation
Indices: 261131--261179 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
261121 CGCAACACAG
261131 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
* * *
261151 TAGCCAAATTTGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
261171 AAGTCAAAT
1 AAGTCAAAT
261180 GTTTTTACGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:263655 original size:4 final size:4
Alignment explanation
Indices: 263646--263687 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
263636 TTTTTCGGCA
* * *
263646 TTAT TTAT TTAT TTAT TTAC TGAT TTAT TTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
263688 TCAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:263850 original size:21 final size:20
Alignment explanation
Indices: 263824--263879 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
263814 TAAGCCCGAT
263824 GCACCTATCATCATTCAAGAG
1 GCACCT-TCATCATTCAAGAG
* *
263845 GCACCTCCTATCGTTCAAGAG
1 GCACCTTC-ATCATTCAAGAG
*
263866 GCCCCTCTCATCAT
1 GCACCT-TCATCAT
263880 CGAAGAAGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (20 bp):
GCACCTTCATCATTCAAGAG
Found at i:263878 original size:42 final size:42
Alignment explanation
Indices: 263831--263929 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
263821 GATGCACCTA
*
263831 TCATCATTCAAGAGGCACCTC-CTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCACCTCTC-ACCGTTCAAGAGGCCCCTC
* * * * *
263873 TCATCA-TCGAAGAAGCCCCTCTCACCGTTCAAGAGGTCTCTG
1 TCATCATTC-AAGAGGCACCTCTCACCGTTCAAGAGGCCCCTC
*
263915 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
263930 TCCTACCCGC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
42 41 0.89
43 3 0.07
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (42 bp):
TCATCATTCAAGAGGCACCTCTCACCGTTCAAGAGGCCCCTC
Found at i:263906 original size:21 final size:21
Alignment explanation
Indices: 263856--263906 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
263846 CACCTCCTAT
* *
263856 CGTTCAAGAGGCCCCTCTCAT
1 CGTTCAAGAAGCCCCTCTCAC
*
263877 C-ATCGAAGAAGCCCCTCTCAC
1 CGTTC-AAGAAGCCCCTCTCAC
263898 CGTTCAAGA
1 CGTTCAAGA
263907 GGTCTCTGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.20
Consensus pattern (21 bp):
CGTTCAAGAAGCCCCTCTCAC
Found at i:265397 original size:28 final size:28
Alignment explanation
Indices: 265352--265405 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
265342 TTTTGATTAA
*
265352 TTGATTTGTAAAAGTTGATTTGTAAAAG
1 TTGATTTGTAAAAGTTGATGTGTAAAAG
** *
265380 TTGATTTGTTTAATTTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
265406 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAG
Found at i:265398 original size:14 final size:14
Alignment explanation
Indices: 265352--265388 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
265342 TTTTGATTAA
265352 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
265366 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
265380 TTGATTTGT
1 TTGATTTGT
265389 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:265452 original size:80 final size:74
Alignment explanation
Indices: 265302--265454 Score: 207
Period size: 80 Copynumber: 2.0 Consensus size: 74
265292 TTTTACATTG
*
265302 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTAAAAGT
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTAATTTGTAAAAGT
265367 TGATTTGTA
66 TGATTTGTA
* * * *
265376 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTAATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAG-A-T-TTATTTT--TTGATTAATTAATTTGT
265441 AAAAGTTGATTTGT
60 AAAAGTTGATTTGT
265455 TGTTTCTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 17 0.25
75 14 0.21
76 1 0.01
77 1 0.01
78 6 0.09
80 29 0.43
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.50
Consensus pattern (74 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTAATTTGTAAAAGT
TGATTTGTA
Found at i:265869 original size:18 final size:18
Alignment explanation
Indices: 265846--265881 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
265836 AAGCCGGTTG
* *
265846 TGATTGGGATTTTGATTT
1 TGATTGCGAATTTGATTT
265864 TGATTGCGAATTTGATTT
1 TGATTGCGAATTTGATTT
265882 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.25, T:0.53
Consensus pattern (18 bp):
TGATTGCGAATTTGATTT
Found at i:268160 original size:24 final size:24
Alignment explanation
Indices: 268133--268186 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
268123 CTATCACATC
* *
268133 ATCAAAATCTGAGTATTCTCCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* * *
268157 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
268181 ATCAAA
1 ATCAAA
268187 TTTTGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:268923 original size:14 final size:15
Alignment explanation
Indices: 268887--268924 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
268877 GAAATCATTG
268887 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
268902 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
268917 AAAAATTA
1 AAAAATTA
268925 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:269106 original size:19 final size:19
Alignment explanation
Indices: 269082--269153 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
269072 ATTAAAACCT
269082 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
269101 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
269120 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
269141 GTTGCGAATTTGA
1 GTTGCGAATTTGA
269154 CTATCGCGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 36 0.72
20 1 0.02
21 13 0.26
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:269163 original size:20 final size:22
Alignment explanation
Indices: 269120--269175 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
269110 TTGAAATTCA
*
269120 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTATTCCGC
269141 GTTGCGAATTTGACTA-T-CGC
1 GTTGCGAATTTGACTATTCCGC
269161 GTTGCGAATTTGACT
1 GTTGCGAATTTGACT
269176 TCTGTGTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 18 0.55
21 14 0.42
22 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (22 bp):
GTTGCGAATTTGACTATTCCGC
Found at i:269184 original size:20 final size:19
Alignment explanation
Indices: 269082--269187 Score: 90
Period size: 19 Copynumber: 5.4 Consensus size: 19
269072 ATTAAAACCT
* *
269082 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
* *
269101 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTG-ACTTCGC
*
269120 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTG-ACTT-CGC
269141 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
*
269161 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
269181 GTTGCGA
1 GTTGCGA
269188 TTTACAAATT
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
19 38 0.47
20 29 0.36
21 13 0.16
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:273502 original size:35 final size:35
Alignment explanation
Indices: 273455--273568 Score: 169
Period size: 35 Copynumber: 3.3 Consensus size: 35
273445 CCATTATCAT
* * *
273455 TTTTC-AACAAACATCTACC-AACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
273489 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
273524 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
273559 TTTTTCAAAG
1 -TTTTCAAAG
273569 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
34 5 0.07
35 53 0.72
36 16 0.22
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:273525 original size:21 final size:21
Alignment explanation
Indices: 273501--273561 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
273491 TTCAAAGAAA
273501 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
273522 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
273536 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
273557 CATTT
1 CATTT
273562 TTCAAAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:273582 original size:34 final size:35
Alignment explanation
Indices: 273452--273595 Score: 140
Period size: 35 Copynumber: 4.2 Consensus size: 35
273442 ATCCCATTAT
*
273452 CATTTTTCAACA-AACA-TCTACC-AACTTTGAAAAA
1 CATTTTTCAA-AGAACAGT-TACCAAACTTTGAAAAC
*
273486 C-TATTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CAT-TTTTCAAAG-AACAGTTACCAAACTTTGAAAAC
*
273522 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAG-AACAGTTACCAAACTTTGAAAAC
***
273557 CATTTTTCAAAG-TTGGTTACCAAAC-TTGAAAAC
1 CATTTTTCAAAGAACAGTTACCAAACTTTGAAAAC
273590 CATTTT
1 CATTTT
273596 AACAATCTCC
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
33 16 0.16
34 17 0.17
35 43 0.44
36 22 0.22
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (35 bp):
CATTTTTCAAAGAACAGTTACCAAACTTTGAAAAC
Found at i:278046 original size:37 final size:36
Alignment explanation
Indices: 277983--278102 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
277973 ATCCCATTAT
* *
277983 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
* *
278019 TATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
278055 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
278090 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
278103 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 28 0.37
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:278059 original size:21 final size:21
Alignment explanation
Indices: 278035--278094 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
278025 TCAAAGAAAT
278035 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
*
278056 ATTT-TCAAA----G-AAA-C
1 ATTTACCAAACTTTGAAAACC
278070 ATTTACCAAACTTTGAAAACC
1 ATTTACCAAACTTTGAAAACC
278091 ATTT
1 ATTT
278095 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTTACCAAACTTTGAAAACC
Found at i:278068 original size:35 final size:36
Alignment explanation
Indices: 277983--278129 Score: 169
Period size: 35 Copynumber: 4.2 Consensus size: 36
277973 ATCCCATTAT
* * *
277983 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAATATTTACCAAACTTTG-AAAAC
*
278019 TATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
*
278055 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
* **
278090 CATTTTTTCAAAG--TTGGTTACCAAAC-TTGAAAAC
1 CA-TTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
278124 CATTTT
1 CATTTT
278130 AACATGGAAG
Statistics
Matches: 98, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
33 4 0.04
34 10 0.10
35 43 0.44
36 13 0.13
37 28 0.29
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAATATTTACCAAACTTTGAAAAC
Found at i:278100 original size:72 final size:68
Alignment explanation
Indices: 277986--278133 Score: 183
Period size: 72 Copynumber: 2.1 Consensus size: 68
277976 CCATTATCAT
*
277986 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAATATTTACCAAACTTTGA
1 TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG--ATAGTTACCAAAC-TTGA
278051 AAACCA
63 AAACCA
* * * * *
278057 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCATTTTTTCAAAGTTGGTTACCAAACTTGAA
1 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA-TTTTTCAAAGATAGTTACCAAACTTGAA
278121 AACCA
64 AACCA
278126 TTTT-AACA
1 TTTTCAACA
278134 TGGAAGAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
67 3 0.04
69 14 0.21
70 10 0.15
71 11 0.16
72 30 0.44
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (68 bp):
TTTTCAACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGATAGTTACCAAACTTGAAAA
CCA
Found at i:280614 original size:21 final size:21
Alignment explanation
Indices: 280545--280617 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
280535 ATTTCTCAAT
** *
280545 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
*
280565 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
280586 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
280607 TCGCAATGCGA
1 TCGCAATGCGA
280618 TACTGACTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 11 0.23
21 36 0.77
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:280630 original size:41 final size:39
Alignment explanation
Indices: 280585--280678 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 39
280575 AATTTGGAAA
* * *
280585 ATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATAT--AAAATCGCAACGCGATACTGACT
280626 ATCGCAACGCGATAATATAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCG--AATATAAAATCGCAACGCGATACTGACT
*
280667 TTCGCAACGCGA
1 ATCGCAACGCGA
280679 TACTGATTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 1 0.02
41 42 0.89
43 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (39 bp):
ATCGCAACGCGAATATAAAATCGCAACGCGATACTGACT
Found at i:280631 original size:20 final size:20
Alignment explanation
Indices: 280606--280684 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
280596 AATTTGGAAA
*
280606 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * **
280626 ATCGCAACGCGATAATATAAA
1 ATCGCAACGCGATACT-GACT
280647 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
280667 TTCGCAACGCGATACTGA
1 ATCGCAACGCGATACTGA
280685 TTCAATAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 32 0.67
21 16 0.33
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:280679 original size:41 final size:41
Alignment explanation
Indices: 280603--280680 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
280593 GCGAATTTGG
*
280603 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAT
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAT
*
280644 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
280681 CTGATTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAT
Found at i:293389 original size:23 final size:23
Alignment explanation
Indices: 293353--293436 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
293343 TAGATGAATT
* * *
293353 GAAGAATAATAAATGGGTTTATG
1 GAAGAAAAAGAAATGAGTTTATG
*
293376 GAAGAAGAAGAAATGAGTTTATG
1 GAAGAAAAAGAAATGAGTTTATG
293399 GAAGAAAAAGAAATGAGTTTATG
1 GAAGAAAAAGAAATGAGTTTATG
293422 GAAGAAAAAGAAATG
1 GAAGAAAAAGAAATG
293437 GAAGAAGCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.21
Consensus pattern (23 bp):
GAAGAAAAAGAAATGAGTTTATG
Found at i:293468 original size:58 final size:57
Alignment explanation
Indices: 293379--293490 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 57
293369 GTTTATGGAA
293379 GAAGAAGAAATGAGTTTATGGAAGAAAAAG-AAATGAGTTTATGGAAGAAAAAGAAATG
1 GAAGAAGAAATGAGTTTATGGAAGAAAAAGAAAAT--GTTTATGGAAGAAAAAGAAATG
* * *
293437 GAAGAAGCAATGAGTTTATGGAAGAAGAAGAAAATGTTTATGGAAGAAGAAGAA
1 GAAGAAGAAATGAGTTTATGGAAGAAAAAGAAAATGTTTATGGAAGAAAAAGAA
293491 TGGTTCAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 18 0.36
58 28 0.56
59 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.29, T:0.19
Consensus pattern (57 bp):
GAAGAAGAAATGAGTTTATGGAAGAAAAAGAAAATGTTTATGGAAGAAAAAGAAATG
Found at i:294441 original size:26 final size:26
Alignment explanation
Indices: 294331--294433 Score: 197
Period size: 26 Copynumber: 4.0 Consensus size: 26
294321 ATTTTAATCA
*
294331 TTATTTATTAAATTAACATAAATAAC
1 TTATTGATTAAATTAACATAAATAAC
294357 TTATTGATTAAATTAACATAAATAAC
1 TTATTGATTAAATTAACATAAATAAC
294383 TTATTGATTAAATTAACATAAATAAC
1 TTATTGATTAAATTAACATAAATAAC
294409 TTATTGATTAAATTAACATAAATAA
1 TTATTGATTAAATTAACATAAATAA
294434 TATCTTGAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (26 bp):
TTATTGATTAAATTAACATAAATAAC
Found at i:310361 original size:36 final size:36
Alignment explanation
Indices: 310287--310366 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
310277 TACCAAACCT
* **
310287 GTCCCCATCCCCGTTTAACATAAACGGTTTTTTCCC
1 GTCCCCGTCCCCGTTTAACATAAACAATTTTTTCCC
* *
310323 GTCTCCGTCCCCGTTTAGCATAAACAA-TTTTTCTCC
1 GTCCCCGTCCCCGTTTAACATAAACAATTTTTTC-CC
310359 GTCCCCGT
1 GTCCCCGT
310367 TTAATTCGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.17, C:0.36, G:0.12, T:0.34
Consensus pattern (36 bp):
GTCCCCGTCCCCGTTTAACATAAACAATTTTTTCCC
Found at i:311088 original size:101 final size:101
Alignment explanation
Indices: 310913--311103 Score: 357
Period size: 101 Copynumber: 1.9 Consensus size: 101
310903 AATTGCATAA
*
310913 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATGTCA
1 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
310978 TGATTTTTTTATCATTTTTACAAAATTATAACATCC
66 TGATTTTTTTATCATTTTTACAAAATTATAACATCC
311014 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
1 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
311079 T-ATATTTTTTATCATTTTTACAAAA
66 TGAT-TTTTTTATCATTTTTACAAAA
311104 ATGATAACTG
Statistics
Matches: 88, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
100 2 0.02
101 86 0.98
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (101 bp):
ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
TGATTTTTTTATCATTTTTACAAAATTATAACATCC
Found at i:313148 original size:422 final size:422
Alignment explanation
Indices: 312364--313640 Score: 2160
Period size: 422 Copynumber: 3.0 Consensus size: 422
312354 TCAATTTGTC
* * *
312364 ACATGATGTACCGGATATATAACATGGACTTTGGAACTATTTACATAACATTTTGCCCAGTTATA
1 ACATGATGTACCGAATATATAACATAGACTTTGGAACTATTTACATAGCATTTTGCCCAGTTATA
*
312429 GCTACTGTGAATTGTAGAATCTATTTTGTAAGTGACACCCTTAAAAACATAGTTATTCCTTTGCT
66 GCTACTGTGAATTGTAGAATCTGTTTTGTAAGTGACACCCTTAAAAACATAGTTATTCCTTTGCT
312494 TCCAGATGTGCCAAATAAGAGCAGAAAAAAAGGAAGACCAAGGAAGATCGCCATCACTTACGGGT
131 TCCAGATGTGCCAAATAAGAGCAGAAAAAAAGGAAGACCAAGGAAGATCGCCATCACTTACGGGT
* *
312559 TGTTGCTTCTGTGATCCATGATTGAAGATCAATACCGAAGAAACAAGCATATGTGGAATGTGGAA
196 TGTTGCTTCTGTGATCCATGATTGAAGATCAATACCGAAGAAACTAGCATATGCGGAATGTGGAA
* * *
312624 CAACAAGCAACCACATGTTTCGGCTGGGTGAGCAATCACACAACACATGAATTACTGATTACATG
261 CAACACGCAACCACAGGTTTCGACTGGGTGAGCAATCACACAACACATGAATTACTGATTACATG
*
312689 GCTGCGCCACAAGTCGCACAGGAGTAGTCATTTGTCAGCATTTGCCTTCCACGTTCATAGTTTGT
326 GCTGCGCCACAAGTCGCACAGGAGTAGTCATTTGTCAGCATTTGCCTTCCGCGTTCATAGTTTGT
312754 CATGATATTTTCTTTATAAGCAAGCCATATGA
391 CATGATATTTTCTTTATAAGCAAGCCATATGA
312786 ACATGATGTACCGAATATATAACATAGACTTTGGAACTATTTACATAGCATTTTGCCCAGTTATA
1 ACATGATGTACCGAATATATAACATAGACTTTGGAACTATTTACATAGCATTTTGCCCAGTTATA
312851 GCTACTGTGAATTGTAGAATCTGTTTTGTAAGTGACACCCTTAAAAACATAGTTATTCCTTTGCT
66 GCTACTGTGAATTGTAGAATCTGTTTTGTAAGTGACACCCTTAAAAACATAGTTATTCCTTTGCT
* *
312916 TCCGGATGTGCCAAATAAGAGCAGAAAAAAAGGAAGACCAAGGAAGATCGCCATCACTTACGGTT
131 TCCAGATGTGCCAAATAAGAGCAGAAAAAAAGGAAGACCAAGGAAGATCGCCATCACTTACGGGT
312981 TGTTGCTTCTGTGATCCATGATTGAAGATCAATACCGAAGAAACTAGCATATGCGGAATGTGGAA
196 TGTTGCTTCTGTGATCCATGATTGAAGATCAATACCGAAGAAACTAGCATATGCGGAATGTGGAA
*
313046 CAACACGCAACCACAGGTTTCGACTAGGTGAGCAATCACACAACACATGAATTACTGATTACATG
261 CAACACGCAACCACAGGTTTCGACTGGGTGAGCAATCACACAACACATGAATTACTGATTACATG
*
313111 GATGCGCCACAAGTCGCACAGGAGTAGTCATTTGTCAGCATTTGCCTTCCGCGTTCATAGTTTGT
326 GCTGCGCCACAAGTCGCACAGGAGTAGTCATTTGTCAGCATTTGCCTTCCGCGTTCATAGTTTGT
313176 CATGATATTTTCTTTATAAGCAAGCCATATGA
391 CATGATATTTTCTTTATAAGCAAGCCATATGA
*
313208 ACATGATGTACC-AGATATATAACATAGACTTTGGAACTATTTACATAGCATTTTTCCCAGTTAT
1 ACATGATGTACCGA-ATATATAACATAGACTTTGGAACTATTTACATAGCATTTTGCCCAGTTAT
* *
313272 AGCTACTGTGAATTGTAGAATCTGTTTTGTAAGTGACACCCTTAAAAACATAGTCATTCATTTGC
65 AGCTACTGTGAATTGTAGAATCTGTTTTGTAAGTGACACCCTTAAAAACATAGTTATTCCTTTGC
* * *
313337 TTCCAGATGTGCCAAATAAGAGCAGTAAAAAAGGAAGACCAAGGAGGATCGCCATTACTTACGGG
130 TTCCAGATGTGCCAAATAAGAGCAGAAAAAAAGGAAGACCAAGGAAGATCGCCATCACTTACGGG
*
313402 TTGTTGCTTCTGAATATTTTGTGTGATCCATGATTGAAGATCAATACCGAAGAAACTAACATATG
195 TTGTTGCTTC-----------TGTGATCCATGATTGAAGATCAATACCGAAGAAACTAGCATATG
** * *
313467 CAAAATGTGGAACAACACGCAACCACAGGTTTCGACTGGGTGGGCAATCACGCAACACATGAATT
249 CGGAATGTGGAACAACACGCAACCACAGGTTTCGACTGGGTGAGCAATCACACAACACATGAATT
* * * *
313532 ACTGATTCCATGGCTGCGCCACAAGTCGCACAGGAGCAGTCATTTGTTAGCATTCGCCTTCCGCG
314 ACTGATTACATGGCTGCGCCACAAGTCGCACAGGAGTAGTCATTTGTCAGCATTTGCCTTCCGCG
* *
313597 TTCATAGTTTGTCATGATCTTTTCTTTATAAGCAAACCATATGA
379 TTCATAGTTTGTCATGATATTTTCTTTATAAGCAAGCCATATGA
313641 TCCTTCAAAT
Statistics
Matches: 808, Mismatches: 35, Indels: 13
0.94 0.04 0.02
Matches are distributed among these distances:
421 1 0.00
422 602 0.75
433 205 0.25
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (422 bp):
ACATGATGTACCGAATATATAACATAGACTTTGGAACTATTTACATAGCATTTTGCCCAGTTATA
GCTACTGTGAATTGTAGAATCTGTTTTGTAAGTGACACCCTTAAAAACATAGTTATTCCTTTGCT
TCCAGATGTGCCAAATAAGAGCAGAAAAAAAGGAAGACCAAGGAAGATCGCCATCACTTACGGGT
TGTTGCTTCTGTGATCCATGATTGAAGATCAATACCGAAGAAACTAGCATATGCGGAATGTGGAA
CAACACGCAACCACAGGTTTCGACTGGGTGAGCAATCACACAACACATGAATTACTGATTACATG
GCTGCGCCACAAGTCGCACAGGAGTAGTCATTTGTCAGCATTTGCCTTCCGCGTTCATAGTTTGT
CATGATATTTTCTTTATAAGCAAGCCATATGA
Found at i:313916 original size:2 final size:2
Alignment explanation
Indices: 313909--313943 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
313899 ATATCGTTTA
313909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
313944 AATACTGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:328407 original size:18 final size:18
Alignment explanation
Indices: 328384--328418 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
328374 CTAGGAGATT
328384 TGAACATA-AATGATAAGA
1 TGAACATACAA-GATAAGA
328402 TGAACATACAAGATAAG
1 TGAACATACAAGATAAG
328419 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (18 bp):
TGAACATACAAGATAAGA
Found at i:329579 original size:149 final size:149
Alignment explanation
Indices: 329309--329623 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 149
329299 GAGTCGAGGG
* *
329309 TCTACGCGGTCTTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
329374 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTAAGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTAAGTGGTCCTTATGGACATCATTA
329439 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
329458 TCTACGCGGTCCTTCGGGATATATATATATT-TTGTGGAACATGTGTGAAGTCTTGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTT-TGGAACATGTGTGAAGTCTTGAAAGACACA
*
329522 TACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTAAGTGGTCCTTATGGACATCATT
329587 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
329607 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
329624 TGCAATTATA
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
148 3 0.02
149 155 0.98
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAAGAATTCTAAGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:329624 original size:23 final size:23
Alignment explanation
Indices: 329591--329635 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
329581 ATCATTATAT
*
329591 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
329614 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
329636 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:334283 original size:21 final size:21
Alignment explanation
Indices: 334259--334301 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
334249 GGACAAGGTG
334259 CAGTACATGTGTGCCTACAGT
1 CAGTACATGTGTGCCTACAGT
334280 CAGTACATGTGTGCCTACAGT
1 CAGTACATGTGTGCCTACAGT
334301 C
1 C
334302 TCTCCTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (21 bp):
CAGTACATGTGTGCCTACAGT
Found at i:340155 original size:16 final size:16
Alignment explanation
Indices: 340117--340197 Score: 51
Period size: 16 Copynumber: 5.1 Consensus size: 16
340107 TTTATCTATT
*
340117 ATTTTATAAAAT-ATA
1 ATTTTATTAAATAATA
* *
340132 ATGATTATTAGATAATA
1 AT-TTTATTAAATAATA
*
340149 ATTTTATAAAAT-ATA
1 ATTTTATTAAATAATA
* **
340164 ATGATTATTTTATAATA
1 AT-TTTATTAAATAATA
*
340181 ATTTTATAAAAT-ATA
1 ATTTTATTAAATAATA
340196 AT
1 AT
340198 GATCATTTTA
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
15 12 0.25
16 26 0.54
17 10 0.21
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
ATTTTATTAAATAATA
Found at i:340206 original size:32 final size:32
Alignment explanation
Indices: 340117--340211 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
340107 TTTATCTATT
**
340117 ATTTTATAAAATATAATGATTATTAGATAATA
1 ATTTTATAAAATATAATGATTATTTTATAATA
340149 ATTTTATAAAATATAATGATTATTTTATAATA
1 ATTTTATAAAATATAATGATTATTTTATAATA
*
340181 ATTTTATAAAATATAATGATCATTTTATAAT
1 ATTTTATAAAATATAATGATTATTTTATAAT
340212 TTAAAAAATT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (32 bp):
ATTTTATAAAATATAATGATTATTTTATAATA
Found at i:343827 original size:65 final size:65
Alignment explanation
Indices: 343712--343839 Score: 193
Period size: 65 Copynumber: 2.0 Consensus size: 65
343702 GTTCAAGCCA
* * *
343712 TTAAGATACATTGATTATTAGTAAAGAATAAAGATAGCAGTGCACCAACCGTAGGGTATACCCGT
1 TTAAGATACATAGATTATTAGTAAAGAATAAAGATAGCAGGGCACAAACCGTAGGGTATACCCGT
* * * *
343777 TTAAGATACATAGATTATTGGTAAATAATAAAGATAGTAGGGCATAAACCGTAGGGTATACCC
1 TTAAGATACATAGATTATTAGTAAAGAATAAAGATAGCAGGGCACAAACCGTAGGGTATACCC
343840 ATCTAAAAGA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (65 bp):
TTAAGATACATAGATTATTAGTAAAGAATAAAGATAGCAGGGCACAAACCGTAGGGTATACCCGT
Found at i:345570 original size:2 final size:2
Alignment explanation
Indices: 345565--345589 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
345555 ACACACACAC
345565 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
345590 AAGTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:350430 original size:13 final size:12
Alignment explanation
Indices: 350393--350424 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
350383 TTGTGACCCT
*
350393 AAATAAACATAA
1 AAATGAACATAA
350405 AAATGAACATAA
1 AAATGAACATAA
350417 AAATGAAC
1 AAATGAAC
350425 GTTAAATACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (12 bp):
AAATGAACATAA
Found at i:355842 original size:28 final size:28
Alignment explanation
Indices: 355799--355877 Score: 140
Period size: 28 Copynumber: 2.8 Consensus size: 28
355789 TGGAGGAGTC
* *
355799 GTATAAAACGCAATAAGCCAAAGAATTT
1 GTATAAAACACCATAAGCCAAAGAATTT
355827 GTATAAAACACCATAAGCCAAAGAATTT
1 GTATAAAACACCATAAGCCAAAGAATTT
355855 GTATAAAACACCATAAGCCAAAG
1 GTATAAAACACCATAAGCCAAAG
355878 CCTATTTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.19
Consensus pattern (28 bp):
GTATAAAACACCATAAGCCAAAGAATTT
Found at i:365780 original size:32 final size:31
Alignment explanation
Indices: 365739--365800 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
365729 ATATAATAGT
*
365739 TATAAAATTTTAAT-AAATTTAATGATTATTC
1 TATAAAA-TTTAATAAAATTTAATAATTATTC
365770 TATAATAATTTAATAAAATTTAATAATTATT
1 TATAA-AATTTAATAAAATTTAATAATTATT
365801 TTATTATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TATAAAATTTAATAAAATTTAATAATTATTC
Found at i:366292 original size:29 final size:30
Alignment explanation
Indices: 366233--366296 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
366223 TAACTTTTTT
*
366233 TTTATCAAATTGTTATAAATAATTATTAAA
1 TTTATCAAATTGTTATAAATAATCATTAAA
*
366263 TTTATCAAATTGTTA-CAATAATCATTAAA
1 TTTATCAAATTGTTATAAATAATCATTAAA
366292 TTTAT
1 TTTAT
366297 ATAAAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTATCAAATTGTTATAAATAATCATTAAA
Found at i:384600 original size:33 final size:33
Alignment explanation
Indices: 384558--384623 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
384548 ATTTTATTAA
*
384558 CAACAATTGTTATTAGTGTATACATATAGTTTG
1 CAACAATTGTGATTAGTGTATACATATAGTTTG
384591 CAACAATTGTGATTAGTGTATACATATAGTTTG
1 CAACAATTGTGATTAGTGTATACATATAGTTTG
384624 GGATGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (33 bp):
CAACAATTGTGATTAGTGTATACATATAGTTTG
Found at i:385639 original size:42 final size:43
Alignment explanation
Indices: 385575--385689 Score: 135
Period size: 42 Copynumber: 2.7 Consensus size: 43
385565 AATCATGGGT
* * *
385575 CTCAATTATAAAGGTAACAAGTGAGATTGATA-AAAG-TAGGCC
1 CTCAATTATAAATGTAAAAAGTGAGATT-AAAGAAAGTTAGGCC
*
385617 CTCAATTATAAATGTAAAAAGTGAGATTAAAGAAAGTTAGGGC
1 CTCAATTATAAATGTAAAAAGTGAGATTAAAGAAAGTTAGGCC
* * *
385660 CTCTATTATAAATATAAAAAAATGAGATTA
1 CTCAATTATAAATGT-AAAAAGTGAGATTA
385690 CAAAAATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
41 2 0.03
42 30 0.48
43 18 0.29
44 13 0.21
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.27
Consensus pattern (43 bp):
CTCAATTATAAATGTAAAAAGTGAGATTAAAGAAAGTTAGGCC
Found at i:385679 original size:43 final size:42
Alignment explanation
Indices: 385579--385721 Score: 137
Period size: 44 Copynumber: 3.3 Consensus size: 42
385569 ATGGGTCTCA
* * * * *
385579 ATTATAAAGGTAACAAGTGAGATTGATAAAAG-TAGGCCCTCA
1 ATTATAAATGTAAAAAGTGAGATT-AAAAAAGTTAGGGCCTCT
385621 ATTATAAATGTAAAAAGTGAGATTAAAGAAAGTTAGGGCCTCT
1 ATTATAAATGTAAAAAGTGAGATTAAA-AAAGTTAGGGCCTCT
* * *
385664 ATTATAAATATAAAAAAATGAGATTACAAAAA-TTAAGGGTCTCT
1 ATTATAAATGT-AAAAAGTGAGATTA-AAAAAGTT-AGGGCCTCT
* *
385708 CTTATAAAGGTAAA
1 ATTATAAATGTAAA
385722 GAAATCAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
41 2 0.02
42 26 0.31
43 23 0.27
44 32 0.38
45 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.27
Consensus pattern (42 bp):
ATTATAAATGTAAAAAGTGAGATTAAAAAAGTTAGGGCCTCT
Found at i:386896 original size:24 final size:24
Alignment explanation
Indices: 386869--386914 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
386859 AATTAATAGG
386869 AATT-TATAAAAAAATATTAAGAAA
1 AATTATATAAAAAAATA-TAAGAAA
*
386893 AATTATATAAAAAGATATAAGA
1 AATTATATAAAAAAATATAAGA
386915 TTAAGTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (24 bp):
AATTATATAAAAAAATATAAGAAA
Found at i:387244 original size:24 final size:23
Alignment explanation
Indices: 387191--387246 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
387181 TCCCTCCCCC
387191 CTTTCTTCTTCTTTGTCATCATCA
1 CTTTCTT-TTCTTTGTCATCATCA
387215 -TCTTCTTTTCTTGTGT-ATCAGTCA
1 CT-TTCTTTTCTT-TGTCATCA-TCA
387239 CTTTCTTT
1 CTTTCTTT
387247 CCCTAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 10 0.36
24 17 0.61
25 1 0.04
ACGTcount: A:0.11, C:0.25, G:0.07, T:0.57
Consensus pattern (23 bp):
CTTTCTTTTCTTTGTCATCATCA
Found at i:393603 original size:2 final size:2
Alignment explanation
Indices: 393596--393623 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
393586 TCTCACAACA
393596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
393624 CATACACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:397267 original size:20 final size:20
Alignment explanation
Indices: 397242--397286 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
397232 AAAATATTCT
397242 AATTAGGTGTTTAGTTTACA
1 AATTAGGTGTTTAGTTTACA
397262 AATTAGGTGTTTAGTTTACA
1 AATTAGGTGTTTAGTTTACA
397282 AATTA
1 AATTA
397287 AGATCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.44
Consensus pattern (20 bp):
AATTAGGTGTTTAGTTTACA
Found at i:405925 original size:175 final size:178
Alignment explanation
Indices: 405624--405982 Score: 528
Period size: 175 Copynumber: 2.0 Consensus size: 178
405614 TATCGCTTTG
* * *
405624 CATCATCTGCAAAGCTACATAAATAAGGGGACGGCATATCAATACGCATATAACCCTACCGGAAT
1 CATCATCTGCAAAGCTACATAAATAAGCGGACAGCATATCAACACGCATATAACCCTACCGGAAT
* * * *
405689 CTAGTATCCCTCAGCTACTCGATTTTGCAGGACACTTTAGGAAAAGCAATGACACCATATAGATT
66 CTAATATCCCTCAGCTACTCGATTTTACAGGACACTTTAGCAAAAGCAATGACAACATATAGATT
* **
405754 TC-GAAACTACAAAATCGGAACTGCAAAATCTTAACATGATAAAAGTAA
131 TCAG-AACTACAAAATCGAAACTGCAAAATCGCAACATGATAAAAGTAA
* * *
405802 CATCATCTGCAAAGCTACATAAAT-A-CGGACAGCATATTAACACGCATATAATCCTACTGGAAT
1 CATCATCTGCAAAGCTACATAAATAAGCGGACAGCATATCAACACGCATATAACCCTACCGGAAT
*
405865 CTAATATTCCT-AGCTACTCGATTTTACAGGACACTTTAGCAAAAGCAATGACAACATATAGATT
66 CTAATATCCCTCAGCTACTCGATTTTACAGGACACTTTAGCAAAAGCAATGACAACATATAGATT
* * *
405929 TCAGAACTACAAAATTGAAACTGCGAATTCGCAACATGATAAAAGTAA
131 TCAGAACTACAAAATCGAAACTGCAAAATCGCAACATGATAAAAGTAA
405977 CATCAT
1 CATCAT
405983 TGAATAACAT
Statistics
Matches: 163, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
175 96 0.59
176 42 0.26
177 1 0.01
178 24 0.15
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (178 bp):
CATCATCTGCAAAGCTACATAAATAAGCGGACAGCATATCAACACGCATATAACCCTACCGGAAT
CTAATATCCCTCAGCTACTCGATTTTACAGGACACTTTAGCAAAAGCAATGACAACATATAGATT
TCAGAACTACAAAATCGAAACTGCAAAATCGCAACATGATAAAAGTAA
Found at i:408829 original size:2 final size:2
Alignment explanation
Indices: 408822--408855 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
408812 TTTCTTATTC
408822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
408856 TAAAAAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:419998 original size:29 final size:30
Alignment explanation
Indices: 419966--420040 Score: 116
Period size: 29 Copynumber: 2.5 Consensus size: 30
419956 AATTCAAAAT
419966 TTAATTAATATTTTATCT-AAATCTAGAGA
1 TTAATTAATATTTTATCTAAAATCTAGAGA
* *
419995 TTAAATAATATTTTATCTAAAATTTAGAGA
1 TTAATTAATATTTTATCTAAAATCTAGAGA
420025 TTAAATTAATATTTTA
1 TT-AATTAATATTTTA
420041 ATTAAGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.41
30 12 0.29
31 12 0.29
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (30 bp):
TTAATTAATATTTTATCTAAAATCTAGAGA
Found at i:420170 original size:33 final size:33
Alignment explanation
Indices: 420130--420213 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
420120 TTCAATGATC
* * * *
420130 AAATATAATAAATTAATCATGTAAATGTGATTG
1 AAATATAATAAATTAATAATATAAATGTGACTA
* *
420163 AAGTATAATAAATTGATAATATAAATGTGACTA
1 AAATATAATAAATTAATAATATAAATGTGACTA
420196 AAATATAATAAATTAATA
1 AAATATAATAAATTAATA
420214 GCATAAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.35
Consensus pattern (33 bp):
AAATATAATAAATTAATAATATAAATGTGACTA
Found at i:420252 original size:32 final size:30
Alignment explanation
Indices: 420166--420265 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 30
420156 GTGATTGAAG
* *
420166 TATAATAAATTGATAATATAAATGTGACTAAAA
1 TATAATAAATTGATTATATAAA--T-AATAAAA
* *
420199 TATAATAAATT-AATAGCATAAATAATAAATA
1 TATAATAAATTGATTA-TATAAATAATAAA-A
420230 TTATAATAAATTGATTATATAAATAATTAAAA
1 -TATAATAAATTGATTATATAAATAA-TAAAA
420262 TATA
1 TATA
420266 TATATATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
30 5 0.09
31 6 0.11
32 22 0.39
33 23 0.41
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (30 bp):
TATAATAAATTGATTATATAAATAATAAAA
Found at i:430812 original size:2 final size:2
Alignment explanation
Indices: 430805--430834 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
430795 CTGGACCATA
430805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
430835 GTACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:431780 original size:23 final size:24
Alignment explanation
Indices: 431749--431801 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
431739 TCACCTTGTC
*
431749 TTATATATATATAATAAAAAAATA
1 TTATATATATAAAATAAAAAAATA
* *
431773 TTAT-TATATAAAATTAAAACATA
1 TTATATATATAAAATAAAAAAATA
*
431796 TAATAT
1 TTATAT
431802 TGTATATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTATATATATAAAATAAAAAAATA
Found at i:432384 original size:19 final size:19
Alignment explanation
Indices: 432327--432386 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
432317 AACATATATC
432327 TATAGGGAGTTTATGCATA
1 TATAGGGAGTTTATGCATA
* * *
432346 TATCATGTGTGTATAT--ATA
1 TAT-A-GGGAGTTTATGCATA
432365 TATAGGGAGTTTATGCATA
1 TATAGGGAGTTTATGCATA
432384 TAT
1 TAT
432387 CAAACTCGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 7 0.23
18 1 0.03
19 15 0.48
20 1 0.03
21 7 0.23
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.42
Consensus pattern (19 bp):
TATAGGGAGTTTATGCATA
Found at i:436362 original size:20 final size:20
Alignment explanation
Indices: 436339--436390 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
436329 TTTGATCACT
436339 AAATGTTTATAAATTATTAA
1 AAATGTTTATAAATTATTAA
436359 AAATGTTTATAAATTATTAA
1 AAATGTTTATAAATTATTAA
*
436379 AAATATTTATAA
1 AAATGTTTATAA
436391 TATTTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (20 bp):
AAATGTTTATAAATTATTAA
Found at i:438315 original size:20 final size:20
Alignment explanation
Indices: 438286--438333 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
438276 GCGATCTCTA
438286 AATCGCAAATCAATTTCCAG
1 AATCGCAAATCAATTTCCAG
* *
438306 AATCGTAAATCAGTTTCCAG
1 AATCGCAAATCAATTTCCAG
*
438326 ATTCGCAA
1 AATCGCAA
438334 CGTGATTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (20 bp):
AATCGCAAATCAATTTCCAG
Found at i:438446 original size:121 final size:123
Alignment explanation
Indices: 438301--438525 Score: 303
Period size: 125 Copynumber: 1.8 Consensus size: 123
438291 CAAATCAATT
* * ** * *
438301 TCCAGAATCGTAAATCAGTTTCCAGATTCGCAACGTGATTTTGAC-TATC-G-CATTGCGGTTTT
1 TCCAGAATCGCAAATCAGTTTCCAGATTCGCAACGAGATAAT-ACAAATCAGTCATTGCGATTTT
438363 AGAAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAATGCGATC
65 AGAAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAATGCGATC
* * **
438422 TCCAGTATCGCAAATCAGTTTCCAGATTCTCAACGAGATAATACAGAATCATGTTGTTGCGATTT
1 TCCAGAATCGCAAATCAGTTTCCAGATTCGCAACGAGATAATACA-AATCA-GTCATTGCGATTT
*
438487 TAGAAAATCGCAATGCGAATATGTAAATCGCAACTCGAT
64 TAGAAAATCGCAATGCGAATATGTAAATCGCAACGCGAT
438526 AATACATAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
120 2 0.02
121 36 0.41
122 3 0.03
124 1 0.01
125 46 0.52
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (123 bp):
TCCAGAATCGCAAATCAGTTTCCAGATTCGCAACGAGATAATACAAATCAGTCATTGCGATTTTA
GAAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGACTATCGCAATGCGATC
Found at i:438622 original size:6 final size:6
Alignment explanation
Indices: 438611--438637 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
438601 GACACGTATT
438611 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
438638 CGAGACGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:439963 original size:6 final size:6
Alignment explanation
Indices: 439927--439951 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
439917 GCACCATCTC
439927 CAACCT CAACCT CAACCT CAACCT C
1 CAACCT CAACCT CAACCT CAACCT C
439952 GACCACCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (6 bp):
CAACCT
Found at i:444776 original size:100 final size:100
Alignment explanation
Indices: 444601--444810 Score: 251
Period size: 100 Copynumber: 2.1 Consensus size: 100
444591 TATCGATAGT
* * * * * * **
444601 GTAATAATAATTACAACTTAATTGGTTAAGATAAAATAGGTGCAACCTATTACGTTAAACTAGTT
1 GTAA-AATAATTACAACTTAACTAGTTAAAATAAAATAAGTACAACCTATTACGTTAAACCAACT
* * *
444666 AGCGGATTGTTTAAAGGTATAATAATAATGTAAACG
65 AGCCGATTGTTTAAAGATATAATAATAATATAAACG
* **
444702 GTAAAATATTTACAACTTAACTAGTTAAAATAAAATAAGTACAACCTATTACGTTACCCCAACTA
1 GTAAAATAATTACAACTTAACTAGTTAAAATAAAATAAGTACAACCTATTACGTTAAACCAACTA
*
444767 -CCGATTTGTTTAAAGATATAATAATAATATAAATG
66 GCCGA-TTGTTTAAAGATATAATAATAATATAAACG
*
444802 ATAAAATAA
1 GTAAAATAA
444811 AATAGGTGCA
Statistics
Matches: 91, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
99 3 0.03
100 84 0.92
101 4 0.04
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (100 bp):
GTAAAATAATTACAACTTAACTAGTTAAAATAAAATAAGTACAACCTATTACGTTAAACCAACTA
GCCGATTGTTTAAAGATATAATAATAATATAAACG
Found at i:444882 original size:75 final size:76
Alignment explanation
Indices: 444727--444960 Score: 244
Period size: 76 Copynumber: 3.1 Consensus size: 76
444717 CTTAACTAGT
* * ** * * *
444727 TAAAATAAAATAAGTACAACCTATTACGTTACCCCAACTACCGATTTGTTTAAAGATATAATAAT
1 TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACTGATTTGTTTAAAGATATAATAAT
* *
444792 AATATAAA-TG
66 AATGTAAACAG
* * *
444802 ATAAAATAAAATAGGTGCAACCTATTACG-TAAACTAGCTACTGGTTTGTTTAAAGGTAAAATAA
1 -TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACTGATTTGTTTAAAGATATAATAA
444866 TAATGTAAACAG
65 TAATGTAAACAG
* ** *
444878 TAAAATAAAATAGGCGTTACCTATTACGTTAAACTAGCTA-TCGATTTGTTCAAA-ATTATAATA
1 TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACT-GATTTGTTTAAAGA-TATAATA
*
444941 ATGAA-GTAAACGG
64 AT-AATGTAAACAG
444954 TAAAATA
1 TAAAATA
444961 TTTACAACTT
Statistics
Matches: 133, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
75 61 0.46
76 70 0.53
77 2 0.02
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (76 bp):
TAAAATAAAATAGGTGCAACCTATTACGTTAAACTAGCTACTGATTTGTTTAAAGATATAATAAT
AATGTAAACAG
Found at i:445118 original size:178 final size:175
Alignment explanation
Indices: 444803--445129 Score: 457
Period size: 178 Copynumber: 1.9 Consensus size: 175
444793 ATATAAATGA
* * *
444803 TAAAATAAAATAGGTGCAACCTATTACGTAAACTAGCTACTGGTTTGTTTAAAGGTAAAATAATA
1 TAAAATAAAATAAGCGCAACCTATTACGTAAACTAGCTACTGGTTTGTTTAAAGATAAAATAATA
* *
444868 ATGTAAACAGTAAAATAAAATAGGCGTTACCTATTACGTTAAACTAGCTATCGATTTGTTCAAAA
66 ATGTAAACAGTAAAATAAAATAGACGCTACCTATTACGTTAAACTAGCTATCGATTTGTTCAAAA
*
444933 TTATAATAATGAA-GTAAACGGTAAAATATTTACAACTTAACCGGT
131 GTATAATAAT-AATGTAAACGGTAAAATATTTACAACTTAACCGGT
*
444978 TAAAATAAAATAAGCGCAACCTATTACGTTAAACTAGCTA-TCGGTTTGTTTAAAGATATAATAA
1 TAAAATAAAATAAGCGCAACCTATTACG-TAAACTAGCTACT-GGTTTGTTTAAAGATAAAATAA
* *
445042 TAATGTAATCGGTTTAAAATAAAATAGACGCTACCTATTACGTTAAACTTA-CTA-C-ATGTTTG
64 TAATGTAAACAG--TAAAATAAAATAGACGCTACCTATTACGTTAAAC-TAGCTATCGA--TTTG
*
445104 TTTAAAAGTATAATAATAATGTAAAC
124 TTCAAAAGTATAATAATAATGTAAAC
445130 AATAAATTAA
Statistics
Matches: 134, Mismatches: 10, Indels: 13
0.85 0.06 0.08
Matches are distributed among these distances:
175 27 0.20
176 42 0.31
177 3 0.02
178 60 0.45
179 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (175 bp):
TAAAATAAAATAAGCGCAACCTATTACGTAAACTAGCTACTGGTTTGTTTAAAGATAAAATAATA
ATGTAAACAGTAAAATAAAATAGACGCTACCTATTACGTTAAACTAGCTATCGATTTGTTCAAAA
GTATAATAATAATGTAAACGGTAAAATATTTACAACTTAACCGGT
Found at i:445179 original size:76 final size:76
Alignment explanation
Indices: 444977--445214 Score: 275
Period size: 76 Copynumber: 3.1 Consensus size: 76
444967 ACTTAACCGG
* * *
444977 TTAAAATAAAATA-AGCGCAACCTATTACGTTAAACTAGCTATCGGTTTGTTT-AAAGATATAAT
1 TTAAAATAAAATAGA-CGCTACATATTACGTTAAACTAGCTACCGGTTTGTTTAAAAG-TATAAT
* *
445040 AATAATGTAATCGGT
64 AATAATGTAAAC--A
* **
445055 TTAAAATAAAATAGACGCTACCTATTACGTTAAACTTA-CTACATGTTTGTTTAAAAGTATAATA
1 TTAAAATAAAATAGACGCTACATATTACGTTAAAC-TAGCTACCGGTTTGTTTAAAAGTATAATA
445119 ATAATGTAAACA
65 ATAATGTAAACA
* * ** * * *
445131 ATAAATTAAAATAGGTGCTACATATTATGTTAAACTGGCTACCGGTTTGTTTAAATGTATAATAA
1 TTAAAATAAAATAGACGCTACATATTACGTTAAACTAGCTACCGGTTTGTTTAAAAGTATAATAA
445196 TAATGTAAACA
66 TAATGTAAACA
445207 TTAAAATA
1 TTAAAATA
445215 TTTACAACTT
Statistics
Matches: 138, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
75 1 0.01
76 70 0.51
78 60 0.43
79 7 0.05
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (76 bp):
TTAAAATAAAATAGACGCTACATATTACGTTAAACTAGCTACCGGTTTGTTTAAAAGTATAATAA
TAATGTAAACA
Found at i:445327 original size:76 final size:75
Alignment explanation
Indices: 445232--445542 Score: 322
Period size: 76 Copynumber: 4.1 Consensus size: 75
445222 CTTAACCGGT
* * * * *
445232 TAAAATAAAAGAGGAGCAACCTACTACGTTAAACTAGCTACTAGTTTGTTTAAAGATATAATAAT
1 TAAAATAAAATA-TAGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
445297 AATGTAAACGA
65 AATGTAAACGA
* * *
445308 TAAAATAAAATATACGCAACTTATTATGTTAAACTAGGTACCAGTTTGTTT-AAGTGTATAATAA
1 TAAAATAAAATATA-GCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAG-GTATAATAA
**
445372 TAATG-AAAATA
64 TAATGTAAACGA
* * * * * *
445383 GTAAAATAAAATATGAACAACCTATTACGTTAAACTAACTACCGGTTTATTTGAAGGTAAAATAA
1 -TAAAATAAAATAT-AGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAA
* *
445448 TAATGTAAATGG
64 TAATGTAAACGA
** * *
445460 TAAAATAAAATAGGGCCTACCTATTACGTTAAACTAGCTACC-GATTTGTTTAATGGTATAATAA
1 TAAAATAAAATATAG-CAACCTATTACGTTAAACTAGCTACCAG-TTTGTTTAAAGGTATAATAA
* *
445524 TAATGTAAGCAA
64 TAATGTAAACGA
445536 TAAAATA
1 TAAAATA
445543 TTTACAACTT
Statistics
Matches: 193, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
75 9 0.05
76 177 0.92
77 7 0.04
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (75 bp):
TAAAATAAAATATAGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAATA
ATGTAAACGA
Found at i:445357 original size:176 final size:176
Alignment explanation
Indices: 445055--445390 Score: 457
Period size: 176 Copynumber: 1.9 Consensus size: 176
445045 TGTAATCGGT
* * *
445055 TTAAAATAAAATAGACGCTACCTATTACGTTAAACTTACTACATGTTTGTTTAAAAGTATAATAA
1 TTAAAATAAAAGAGACGCAACCTACTACGTTAAACTTACTACATGTTTGTTTAAAAGTATAATAA
* ** * *
445120 TAATGTAAACAATAAATTAAAATAGGTGCTACATATTATGTTAAACTGGCTACCGGTTTGTTTAA
66 TAATGTAAACAATAAAATAAAATAGACGCAACATATTATGTTAAACTGGCTACCAGTTTGTTTAA
* *
445185 ATGTATAATAATAATGTAAACATTAAAATATTTACAACTTAACCGG
131 ATGTATAATAATAATGAAAACAGTAAAATATTTACAACTTAACCGG
445231 TTAAAATAAAAGAGGA-GCAACCTACTACGTTAAAC-TAGCTAC-TAGTTTGTTT-AAAGATATA
1 TTAAAATAAAAGA-GACGCAACCTACTACGTTAAACTTA-CTACAT-GTTTGTTTAAAAG-TATA
* * *
445292 ATAATAATGTAAACGATAAAATAAAATATACGCAACTTATTATGTTAAACTAGG-TACCAGTTTG
62 ATAATAATGTAAACAATAAAATAAAATAGACGCAACATATTATGTTAAACT-GGCTACCAGTTTG
* *
445356 TTTAAGTGTATAATAATAATGAAAATAGTAAAATA
126 TTTAAATGTATAATAATAATGAAAACAGTAAAATA
445391 AAATATGAAC
Statistics
Matches: 140, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
175 7 0.05
176 129 0.92
177 4 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (176 bp):
TTAAAATAAAAGAGACGCAACCTACTACGTTAAACTTACTACATGTTTGTTTAAAAGTATAATAA
TAATGTAAACAATAAAATAAAATAGACGCAACATATTATGTTAAACTGGCTACCAGTTTGTTTAA
ATGTATAATAATAATGAAAACAGTAAAATATTTACAACTTAACCGG
Found at i:445508 original size:152 final size:152
Alignment explanation
Indices: 445232--445528 Score: 375
Period size: 152 Copynumber: 2.0 Consensus size: 152
445222 CTTAACCGGT
* * * * *
445232 TAAAATAAAAGAGGAGCAACCTACTACGTTAAACTAGCTACTAGTTTGTTTAAAGATATAATAAT
1 TAAAATAAAAGAGGAACAACCTACTACGTTAAACTAACTACCAGTTTATTTAAAGATAAAATAAT
* * * *
445297 AATGTAAACGATAAAATAAAATATACGCAACTTATTATGTTAAACTAGGTACCAGTTTGTTTAA-
66 AATGTAAACGATAAAATAAAATAGACGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAT
445361 GTGTATAATAATAATGAAAATAG
131 G-GTATAATAATAATGAAAATAG
* * * * * *
445384 TAAAATAAAATATGAACAACCTATTACGTTAAACTAACTACCGGTTTATTTGAAGGTAAAATAAT
1 TAAAATAAAAGAGGAACAACCTACTACGTTAAACTAACTACCAGTTTATTTAAAGATAAAATAAT
* * * *
445449 AATGTAAATGGTAAAATAAAATAG-GGCCTACCTATTACGTTAAACTAGCTACC-GATTTGTTTA
66 AATGTAAACGATAAAATAAAATAGACG-CAACCTATTACGTTAAACTAGCTACCAG-TTTGTTTA
445512 ATGGTATAATAATAATG
129 ATGGTATAATAATAATG
445529 TAAGCAATAA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
151 2 0.02
152 120 0.98
153 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (152 bp):
TAAAATAAAAGAGGAACAACCTACTACGTTAAACTAACTACCAGTTTATTTAAAGATAAAATAAT
AATGTAAACGATAAAATAAAATAGACGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAT
GGTATAATAATAATGAAAATAG
Found at i:445521 original size:328 final size:329
Alignment explanation
Indices: 444978--445642 Score: 869
Period size: 328 Copynumber: 2.0 Consensus size: 329
444968 CTTAACCGGT
* *
444978 TAAAATAAAATAAGCGCAACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATATAATAAT
1 TAAAATAAAATAAGCGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGATATAATAAT
* * * * * * *
445043 AATGTAATCGGTTTAAAATAAAATAGACGCTACCTATTACGTTAAACTTACTACATGTTTGTTTA
66 AATGAAATCAG-TTAAAATAAAATAGACACAACCTATTACGTTAAACTAACTACAGGTTTATTTA
* * * *
445108 AAAGTATAATAATAATGTAAACAATAAATTAAAATAGGTGCTACATATTATGTTAAACTGGCTAC
130 AAAGTAAAATAATAATGTAAACAATAAAATAAAATAGGTGCTACATATTACGTTAAACTAGCTAC
* *
445173 CGGTTTGTTTAAATGTATAATAATAATGTAAACATTAAAATATTTACAACTTAACCGGTTAAAAT
195 CGATTTGTTTAAATGTATAATAATAATGTAAACAATAAAATATTTACAACTTAACCGGTTAAAAT
* *
445238 AAAAGAGGAGCAACCTACTACGTTAAACTAGCTACTAGTTTGTTTA-AAGATATAATAATAATGT
260 AAAAGAGGAGCAACCTACTACGTTAAACTACCTACCAGTTTGTTTACAAG-TATAATAATAATGT
445302 AAACGA
324 AAACGA
* * * *
445308 TAAAATAAAATATA-CGCAACTTATTATGTTAAACTAGGTACCAGTTTGTTT-AAGTGTATAATA
1 TAAAATAAAATA-AGCGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAG-ATATAATA
*
445371 ATAATGAAAAT-AG-TAAAATAAAATATGA-ACAACCTATTACGTTAAACTAACTACCGGTTTAT
64 ATAATG-AAATCAGTTAAAATAAAATA-GACACAACCTATTACGTTAAACTAACTACAGGTTTAT
* * *** *
445433 TTGAAGGTAAAATAATAATGTAAATGGTAAAATAAAATAGG-GCCTACCTATTACGTTAAACTAG
127 TTAAAAGTAAAATAATAATGTAAACAATAAAATAAAATAGGTG-CTACATATTACGTTAAACTAG
*
445497 CTACCGATTTGTTT-AATGGTATAATAATAATGTAAGCAATAAAATATTTACAACTTAACCGGTT
191 CTACCGATTTGTTTAAAT-GTATAATAATAATGTAAACAATAAAATATTTACAACTTAACCGGTT
* * * * * * *
445561 AAAATAAAATAGGTGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTACATGTATAATATTA
255 AAAATAAAAGAGGAGCAACCTACTACGTTAAACTACCTACCAGTTTGTTTACAAGTATAATAATA
*
445626 ATGTAAATGA
320 ATGTAAACGA
445636 TAAAATA
1 TAAAATA
445643 TTTACAACTT
Statistics
Matches: 291, Mismatches: 37, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
327 4 0.01
328 218 0.75
329 7 0.02
330 58 0.20
331 4 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (329 bp):
TAAAATAAAATAAGCGCAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGATATAATAAT
AATGAAATCAGTTAAAATAAAATAGACACAACCTATTACGTTAAACTAACTACAGGTTTATTTAA
AAGTAAAATAATAATGTAAACAATAAAATAAAATAGGTGCTACATATTACGTTAAACTAGCTACC
GATTTGTTTAAATGTATAATAATAATGTAAACAATAAAATATTTACAACTTAACCGGTTAAAATA
AAAGAGGAGCAACCTACTACGTTAAACTACCTACCAGTTTGTTTACAAGTATAATAATAATGTAA
ACGA
Found at i:445755 original size:100 final size:100
Alignment explanation
Indices: 445476--445766 Score: 393
Period size: 100 Copynumber: 2.9 Consensus size: 100
445466 AAAATAGGGC
* * * * *
445476 CTACCTATTACGTTAAACTAGCTACCGATTTGTTTAATGGTATAATAATAATGTAAGCAATAAAA
1 CTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAA
* * ****
445541 TATTTACAACTTAACCGGTTAAAATAAAATAGGTG
66 TATTTACAACTTAATCGATTAAAATAAAATAAACA
* * * *
445576 CTACCTATTACGTTAAACTACCTACCGGTTTGTTTACATGTATAATATTAATGTAAATGATAAAA
1 CTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAA
* *
445641 TATTTACAACTTAATTGATTAAAATAAGATAAACA
66 TATTTACAACTTAATCGATTAAAATAAAATAAACA
* *
445676 CTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAGTAATGTAAACGGTAAAA
1 CTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAA
* *
445741 TATTTACAACTTAATCGTTTGAAATA
66 TATTTACAACTTAATCGATTAAAATA
445767 TTTTTTTAAA
Statistics
Matches: 166, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
100 166 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (100 bp):
CTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAA
TATTTACAACTTAATCGATTAAAATAAAATAAACA
Found at i:446566 original size:108 final size:108
Alignment explanation
Indices: 446392--446723 Score: 393
Period size: 108 Copynumber: 3.1 Consensus size: 108
446382 CCTAGTATGT
* * * *
446392 TAATATTTATTTAAACAAAATAAGTATTTAACCTATTTTGTTGTCATGAGATTTCGAATGCC-CA
1 TAATATTTA--TAAAAAAAATAAGTAATTAACCTATTTTGTTATCATGAGATTTCTAA-GCCTCA
* ** * *
446456 TCAACTTAAACTTTGGTAACATATTATACGCAACCTAATTTGTTGA
63 TCAACTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGA
* *
446502 TAATATTTATAAAAAAAATAAGTAATTAACATATTTTGTTATCATGTGATTTCTAAGCCTCATCA
1 TAATATTTATAAAAAAAATAAGTAATTAACCTATTTTGTTATCATGAGATTTCTAAGCCTCATCA
* * * *
446567 ACTTAAATTTTAGTAACATTTTAGGTGTTACCTAATATGTTGA
66 ACTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGA
* * * *
446610 TAATA-TTA-ATAAAAAATAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAAG-TTACAT
1 TAATATTTATAAAAAAAATAAGTAATTAACCTATTTTGTTATCATGAGATTTCT-AAGCCT-CAT
* * *
446672 TAGCTTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGA
64 CAACTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGA
446717 TAATATT
1 TAATATT
446724 AATGTAAGGT
Statistics
Matches: 190, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
106 40 0.21
107 55 0.29
108 86 0.45
110 9 0.05
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (108 bp):
TAATATTTATAAAAAAAATAAGTAATTAACCTATTTTGTTATCATGAGATTTCTAAGCCTCATCA
ACTTAAACTTTGGTAACATTTTAGGCGCTACCTAATATGTTGA
Found at i:450663 original size:28 final size:28
Alignment explanation
Indices: 450632--450690 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
450622 GCCCACTTTT
450632 AAACATGATAAGAATGAGATTAGTTAAA
1 AAACATGATAAGAATGAGATTAGTTAAA
450660 AAACATGATAAGAATGAGATTAGTTAAA
1 AAACATGATAAGAATGAGATTAGTTAAA
450688 AAA
1 AAA
450691 ATGTTGGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.56, C:0.03, G:0.17, T:0.24
Consensus pattern (28 bp):
AAACATGATAAGAATGAGATTAGTTAAA
Found at i:453628 original size:24 final size:21
Alignment explanation
Indices: 453574--453628 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 21
453564 CAGACAGTAC
*
453574 AAATTTAAGAAATTATATTAA
1 AAATTTAAGAAATTAAATTAA
453595 AAATTT-AGAAATATGAAATTATA
1 AAATTTAAGAAAT-T-AAATTA-A
453618 AAATTTAAGAA
1 AAATTTAAGAA
453629 GTACAATAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.21
21 7 0.24
22 5 0.17
23 7 0.24
24 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
AAATTTAAGAAATTAAATTAA
Found at i:453895 original size:15 final size:15
Alignment explanation
Indices: 453867--453930 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 15
453857 GTTTTCAAAG
453867 TTTGATAAATGTTTC
1 TTTGATAAATGTTTC
453882 TTTGA-AAATAGTTTTC
1 TTTGATAAAT-G-TTTC
453898 AAAGTTTGATAAATGTTTC
1 ----TTTGATAAATGTTTC
*
453917 TTTGAAAAATGTTT
1 TTTGATAAATGTTT
453931 TTCAAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
14 4 0.10
15 19 0.46
16 4 0.10
19 4 0.10
20 6 0.15
21 4 0.10
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (15 bp):
TTTGATAAATGTTTC
Found at i:453933 original size:36 final size:34
Alignment explanation
Indices: 453847--453950 Score: 165
Period size: 35 Copynumber: 3.0 Consensus size: 34
453837 TGACAACCAA
453847 CTTTGAAAATGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAATGTTTTCAAAGTTTGATAAATGTTT
453881 CTTTGAAAATAGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAAT-GTTTTCAAAGTTTGATAAATGTTT
*
453916 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATG-TTTTCAAAGTTTGATAAATGTTT
453951 GGTAGATTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
34 10 0.15
35 34 0.52
36 22 0.33
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.46
Consensus pattern (34 bp):
CTTTGAAAATGTTTTCAAAGTTTGATAAATGTTT
Found at i:458415 original size:22 final size:22
Alignment explanation
Indices: 458390--458432 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
458380 TAAATAGAGA
458390 AATAAAAA-TTAGAATATAATAC
1 AATAAAAATTTA-AATATAATAC
458412 AATAAAAATTTAAATATAATA
1 AATAAAAATTTAAATATAATA
458433 TAAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAAATTTAAATATAATAC
Found at i:467186 original size:61 final size:61
Alignment explanation
Indices: 467115--467237 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
467105 AATAACTTTA
467115 ATAAATAATAAATACAAATAAACATTAATATCAGCTAAAAGATAAACATTATTATTGTCAT
1 ATAAATAATAAATACAAATAAACATTAATATCAGCTAAAAGATAAACATTATTATTGTCAT
467176 ATAAATAATAAATACAAATAAACATTAATATCAGCTAAAAGATAAACATTATTATTGTCAT
1 ATAAATAATAAATACAAATAAACATTAATATCAGCTAAAAGATAAACATTATTATTGTCAT
467237 A
1 A
467238 GGATATTATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.31
Consensus pattern (61 bp):
ATAAATAATAAATACAAATAAACATTAATATCAGCTAAAAGATAAACATTATTATTGTCAT
Found at i:469512 original size:2 final size:2
Alignment explanation
Indices: 469505--469542 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
469495 CGTATTAATA
469505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
469543 TATTAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:469558 original size:12 final size:15
Alignment explanation
Indices: 469497--469545 Score: 68
Period size: 16 Copynumber: 3.4 Consensus size: 15
469487 CTTCATGTCG
469497 TATTA-ATA-ATATA
1 TATTATATATATATA
469510 TA-TATATATATATA
1 TATTATATATATATA
469524 TATATATATATATATA
1 TAT-TATATATATATA
469540 TATTAT
1 TATTAT
469546 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.06
13 5 0.16
14 7 0.22
15 3 0.09
16 15 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTATATATATATA
Found at i:471189 original size:21 final size:21
Alignment explanation
Indices: 471165--471204 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
471155 TAAAACGCCC
*
471165 AATAATAACATTTTCAGTAGA
1 AATAATAACATTTTAAGTAGA
*
471186 AATAATAATATTTTAAGTA
1 AATAATAACATTTTAAGTA
471205 AATTTTTACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTAAGTAGA
Done.